Sequence-specific reconstruction from fragmentary databases using seed sequences: implementation and validation on SAGE, proteome and generic sequencing data

Motivation: DNA assembly programs classically perform an all-against-all comparison of reads to identify overlaps, followed by a multiple sequence alignment and generation of a consensus sequence. If the aim is to assemble a particular segment, instead of a whole genome or transcriptome, a target-specific assembly is a more sensible approach. GenSeed is a Perl program that implements a seed-driven recursive assembly consisting of cycles comprising a similarity search, read selection and assembly. The iterative process results in a progressive extension of the original seed sequence. GenSeed was tested and validated on many applications, including the reconstruction of nuclear genes or segments, full-length transcripts, and extrachromosomal genomes. The robustness of the method was confirmed through the use of a variety of DNA and protein seeds, including short sequences derived from SAGE and proteome projects.

The role of carbon impurities on the Si(001)-c(4 x 4) surface reconstruction: Theoretical calculations

In this work we employ the state-of-the-art pseudopotential method, within a generalized gradient approximation to the density functional theory, combined with a recently developed method for the calculation of HREELS spectra to study a series of different proposed models for carbon incorporation on the silicon (001) surface. A fully discussion on the geometry, energetics and specially the comparison between experimental and theoretical STM images and electron energy loss spectra indicate that the Si(100)-c(4 x 4) is probably induced by Si-C surface dinners, in agreement with recent experimental findings. (C) 2009 Elsevier B.V. All rights reserved.

Performance Improvement of Tomographic Image Reconstruction Based on DSP Processors

This paper presents the use of a multiprocessor architecture for the performance improvement of tomographic image reconstruction. Image reconstruction in computed tomography (CT) is an intensive task for single-processor systems. We investigate the filtered image reconstruction suitability based on DSPs organized for parallel processing and its comparison with the Message Passing Interface (MPI) library. The experimental results show that the speedups observed for both platforms were increased in the same direction of the image resolution. In addition, the execution time to communication time ratios (Rt/Rc) as a function of the sample size have shown a narrow variation for the DSP platform in comparison with the MPI platform, which indicates its better performance for parallel image reconstruction.

Recording from Two Neurons: Second-Order Stimulus Reconstruction from Spike Trains and Population Coding

We study the reconstruction of visual stimuli from spike trains, representing the reconstructed stimulus by a Volterra series up to second order. We illustrate this procedure in a prominent example of spiking neurons, recording simultaneously from the two H1 neurons located in the lobula plate of the fly Chrysomya megacephala. The fly views two types of stimuli, corresponding to rotational and translational displacements. Second-order reconstructions require the manipulation of potentially very large matrices, which obstructs the use of this approach when there are many neurons. We avoid the computation and inversion of these matrices using a convenient set of basis functions to expand our variables in. This requires approximating the spike train four-point functions by combinations of two-point functions similar to relations, which would be true for gaussian stochastic processes. In our test case, this approximation does not reduce the quality of the reconstruction. The overall contribution to stimulus reconstruction of the second-order kernels, measured by the mean squared error, is only about 5% of the first-order contribution. Yet at specific stimulus-dependent instants, the addition of second-order kernels represents up to 100% improvement, but only for rotational stimuli. We present a perturbative scheme to facilitate the application of our method to weakly correlated neurons.

Accurate velocity reconstruction for Discontinuous Galerkin approximations of two-phase porous media flows

We consider Discontinuous Galerkin approximations of two-phase, immiscible porous media flows in the global pressure/fractional flow formulation with capillary pressure. A sequential approach is used with a backward Euler step for the saturation equation, equal-order interpolation for the pressure and the saturation, and without any limiters. An accurate total velocity field is recovered from the global pressure equation to be used in the saturation equation. Numerical experiments show the advantages of the proposed reconstruction. To cite this article: A. Ern et al., C R. Acad. Sci. Paris, Ser. 1347 (2009). (C) 2009 Academie des sciences. Published by Elsevier Masson SAS. All rights reserved.

Persuading the Public : A Linguistic Analysis of Barack Obama’s Speech on “Super Tuesday” 2008

This essay examines the persuasive side of language in a speech given by Senator Barack Obama on Super Tuesday in February 2008. It studies how Senator Obama utilizes language to convince and persuade his audience. This is done from an Aristotelian point of view, meaning that the study focuses foremost on how the senator’s word choices relate to Aristotle’s three means of persuasion, ethos, pathos and logos. Those basic guiding principles are relevant to use since Aristotle’s work on the subject of rhetoric is still today one of the most relevant works in that field. The analysis is basically performed through personal observations guided by previous studies, within the frame of Aristotelian rhetoric. The results show how Senator Obama enforces the three means of persuasion through language and how it can be considered persuasive. The study might add to rhetoric studies from a linguistic perspective since it reaches a better understanding of language used in the field of politics, where rhetoric is a prominent component.

The Concept of ’Selling/Buying’ in the Russian Linguistic Picture of the World : from standard to sub-standard

The thesis belongs to the field of lexical semantics studies, associated with describing the Russian linguistic world-image. The research focuses on the universal situation of purchase and sale as reflected in the Russian lexical standard and sub-standard. The work deals also with subjects related to the sphere of social linguistics: the social stratification of the language, the structure of sub-standard, etc. The thesis is a contribution to the description of the Russian linguistic world-image as well as to the further elaboration of the conceptional analysis method. The results are applicable in teaching Russian as a foreign language, particularly in lexis and Russian culture and mentality studies.

A Linguistic Analysis of the Written Production of Second Language Learners : The Variation of Article Usage by Adult Chinese Learners of English

This study aims to test Robertson’s lexical transfer principle, which posits that Chinese learners use demonstratives (particularly this) and the numeral one as markers of definiteness and indefiniteness. This is tested by analysing Chinese learners’ written production collected from the Spoken and Written English Corpus of Chinese Learners 2.0 (SWECCL 2.0). The purpose is to understand the variation of article usage by adult Chinese learners of English. More specifically, the study examines to what extent articles, possessive and demonstrative pronouns are used in Chinese learners’ English and how definite and indefinite articles are used by the Chinese learners. Findings suggest that Robertson’s lexical transfer principle was corroborated by the present study. In addition, Chinese learners prefer to use demonstrative determiners, the possessive determiner our, and the numeral one to perform the function of marking definiteness and indefiniteness. In particular, the learners try to use the demonstrative determiners that and this in the anaphoric function instead of the definite article, and the demonstrative determiner those is frequently used in the cataphoric function. What is more, the learners use the numeral one as a marker of indefiniteness, and it is also used as a marker of definiteness in the anaphoric function. Further, the possessive determiner our is used as a marker of definiteness in larger situation uses referring to something unique. To this end, the study is able to show that the definite article is used to perform the function of marking indefiniteness, and in some particular contexts the definite article functions as a Chinese specifier in Chinese learners’ English. Also, the indefinite article is frequently used in quantifier phrases but is rarely used in other functions. There are three main reasons that may explain why Chinese learners use determiners variously. Firstly, the choice of determiners by Chinese learners is influenced by linguistic contexts. Secondly, because of learning strategies, Chinese learners try to ignore the anaphoric function and cataphoric function that they are not yet ready to process in article usage. Thirdly, interlanguage grammar influences the optionality in the use of articles. 

System for Automated Deduction (SAD): Linguistic and Deductive Peculiarities

In this paper a state of the art of a system of automated deduction called SAD is described . An architecture of SAD corresponds well to a modern vision of the Evidence Algorithm programme, initiated by Academician V.Glushkov.

3D reconstruction through photographs

Humans can perceive three dimension, our world is three dimensional and it is becoming increasingly digital too. We have the need to capture and preserve our existence in digital means perhaps due to our own mortality. We have also the need to reproduce objects or create small identical objects to prototype, test or study them. Some objects have been lost through time and are only accessible through old photographs. With robust model generation from photographs we can use one of the biggest human data sets and reproduce real world objects digitally and physically with printers. What is the current state of development in three dimensional reconstruction through photographs both in the commercial world and in the open source world? And what tools are available for a developer to build his own reconstruction software? To answer these questions several pieces of software were tested, from full commercial software packages to open source small projects, including libraries aimed at computer vision. To bring to the real world the 3D models a 3D printer was built, tested and analyzed, its problems and weaknesses evaluated. Lastly using a computer vision library a small software with limited capabilities was developed.